Over 30 small molecules are available for the treatment of Human Immunodeficiency Virus 1 (HIV-1) infection, targeting the viral proteins reverse transcriptase (RT), protease and integrase, as well as the cellular entry co-receptor, CCR51. Although treatment of HIV-1 with combination small molecule therapy is effective in preventing Acquired Immune Deficiency Syndrome (AIDS), it is not able to eradicate the virus and is associated with a number of short- and long-term side effects2. Alternative therapeutic strategies for long-term viral suppression with low adverse effects are needed.
Small RNAs represent a growing class of molecules with the potential to complement or replace current therapies. They are being evaluated for use in ex vivo gene therapy3 and with advances that have been made in their systemic delivery4, may soon be evaluated for use in combination drug therapy. Many small RNAs, including antisense oligonucleotides (ASONs), ribozymes (Rzs), decoys, aptamers, small nuclear (sn) RNAs, and small interfering (si) or short hairpin (sh) RNAs have been designed with diverse target sites in the HIV-1 replication cycle5. Antisense-based RNAs (ASONs, Rzs, snRNAs, sh/siRNAs) can be designed to target HIV-1 RNA, and several therapeutic candidates have been described.
Rzs targeting HIV-1 RNA have been made by modifying hammerhead, hairpin6 and bacterial RNase P7 motifs. The HDV Rz represents an alternative small Rz motif, that has evolved to function in human cells and has the potential to be used for the development of therapeutic Rzs8. To improve the specificity of the HDV Rz for its target RNA, the SOFA (Specific On/oFf Adaptor) module was engineered9,10 (FIG. 1A). Several SOFA-HDV-Rzs have been identified with the potential to target human11,12, viral9,13,14 and bacterial15 RNAs, including three Rzs that we have evaluated targeting the overlapping Tat/Rev coding sequence of HIV-1 RNA16.
Optimal hammerhead Rz target sites in HIV-1 RNA have been identified using libraries of Rzs with randomized binding arms17,18 and a library of Rzs targeting highly conserved sequences19. Using different methods and datasets to estimate sequence conservation, sets of optimal siRNAs20 or shRNAs21,22 have been identified and two of these studies have reported their conservation estimates in 19 to 21 nt frames20,22. Estimates have also been reported at the nucleotide (nt) level to identify or characterize Rz23, snRNA24 and shRNA25 target sites.
The present description refers to a number of documents, the content of which is herein incorporated by reference in their entirety.